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Dannhorn A, Kazanc E, Flint L, Guo F, Carter A, Hall AR, Jones SA, Poulogiannis G, Barry ST, Sansom OJ, Bunch J, Takats Z, Goodwin RJA. Morphological and molecular preservation through universal preparation of fresh-frozen tissue samples for multimodal imaging workflows. Nat Protoc 2024; 19:2685-2711. [PMID: 38806741 DOI: 10.1038/s41596-024-00987-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/14/2024] [Indexed: 05/30/2024]
Abstract
The landscape of tissue-based imaging modalities is constantly and rapidly evolving. While formalin-fixed, paraffin-embedded material is still useful for histological imaging, the fixation process irreversibly changes the molecular composition of the sample. Therefore, many imaging approaches require fresh-frozen material to get meaningful results. This is particularly true for molecular imaging techniques such as mass spectrometry imaging, which are widely used to probe the spatial arrangement of the tissue metabolome. As high-quality fresh-frozen tissues are limited in their availability, any sample preparation workflow they are subjected to needs to ensure morphological and molecular preservation of the tissues and be compatible with as many of the established and emerging imaging techniques as possible to obtain the maximum possible insights from the tissues. Here we describe a universal sample preparation workflow, from the initial step of freezing the tissues to the cold embedding in a new hydroxypropyl methylcellulose/polyvinylpyrrolidone-enriched hydrogel and the generation of thin tissue sections for analysis. Moreover, we highlight the optimized storage conditions that limit molecular and morphological degradation of the sections. The protocol is compatible with human and plant tissues and can be easily adapted for the preparation of alternative sample formats (e.g., three-dimensional cell cultures). The integrated workflow is universally compatible with histological tissue analysis, mass spectrometry imaging and imaging mass cytometry, as well as spatial proteomic, genomic and transcriptomic tissue analysis. The protocol can be completed within 4 h and requires minimal prior experience in the preparation of tissue samples for multimodal imaging experiments.
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Affiliation(s)
- Andreas Dannhorn
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London, UK
| | - Emine Kazanc
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London, UK
| | - Lucy Flint
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Fei Guo
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
- Safety Innovations, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Alfie Carter
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
- Safety Innovations, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Andrew R Hall
- Safety Innovations, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Stewart A Jones
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | - Simon T Barry
- Bioscience, Discovery, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - Josephine Bunch
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington, UK
| | - Zoltan Takats
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London, UK
| | - Richard J A Goodwin
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK.
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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Islam MM, Rahman MF, Islam A, Afroz MS, Mamun MA, Rahman MM, Maniruzzaman M, Xu L, Sakamoto T, Takahashi Y, Sato T, Kahyo T, Setou M. Elucidating Gender-Specific Distribution of Imipramine, Chloroquine, and Their Metabolites in Mice Kidney Tissues through AP-MALDI-MSI. Int J Mol Sci 2024; 25:4840. [PMID: 38732055 PMCID: PMC11084644 DOI: 10.3390/ijms25094840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Knowledge of gender-specific drug distributions in different organs are of great importance for personalized medicine and reducing toxicity. However, such drug distributions have not been well studied. In this study, we investigated potential differences in the distribution of imipramine and chloroquine, as well as their metabolites, between male and female kidneys. Kidneys were collected from mice treated with imipramine or chloroquine and then subjected to atmospheric pressure matrix-assisted laser desorption ionization-mass spectrometry imaging (AP-MALDI-MSI). We observed differential distributions of the drugs and their metabolites between male and female kidneys. Imipramine showed prominent distributions in the cortex and medulla in male and female kidneys, respectively. Desipramine, one of the metabolites of imipramine, showed significantly higher (*** p < 0.001) distributions in the medulla of the male kidney compared to that of the female kidney. Chloroquine and its metabolites were accumulated in the pelvis of both male and female kidneys. Interestingly, they showed a characteristic distribution in the medulla of the female kidney, while almost no distributions were observed in the same areas of the male kidney. For the first time, our study revealed that the distributions of imipramine, chloroquine, and their metabolites were different in male and female kidneys.
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Affiliation(s)
- Md. Monirul Islam
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
- Institute of Food and Radiation Biology, Atomic Energy Research Establishment, Bangladesh Atomic Energy Commission, Dhaka 1349, Bangladesh
| | - Md Foyzur Rahman
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
| | - Ariful Islam
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
- Department of Biochemistry and Microbiology, School of Health and Life Sciences, North South University, Bashundhara, Dhaka 1229, Bangladesh
- Preppers Co., Ltd., Hamamatsu City 431-3192, Shizuoka, Japan
| | - Mst. Sayela Afroz
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
| | - Md. Al Mamun
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
- Preppers Co., Ltd., Hamamatsu City 431-3192, Shizuoka, Japan
| | - Md. Muedur Rahman
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
- Preppers Co., Ltd., Hamamatsu City 431-3192, Shizuoka, Japan
| | - Md Maniruzzaman
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
| | - Lili Xu
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
| | - Takumi Sakamoto
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
- Preppers Co., Ltd., Hamamatsu City 431-3192, Shizuoka, Japan
| | - Yutaka Takahashi
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
- Preppers Co., Ltd., Hamamatsu City 431-3192, Shizuoka, Japan
- International Mass Imaging Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan
| | - Tomohito Sato
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
- International Mass Imaging Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan
| | - Tomoaki Kahyo
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
- International Mass Imaging Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan; (M.M.I.); (M.F.R.); (A.I.); (M.S.A.); (M.A.M.); (T.S.); (Y.T.); (T.S.); (T.K.)
- Preppers Co., Ltd., Hamamatsu City 431-3192, Shizuoka, Japan
- International Mass Imaging Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan
- Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education and Research Center, 1-20-1 Handayama, Chuo-Ku, Hamamatsu City 431-3192, Shizuoka, Japan
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Chadha R, Guerrero JA, Wei L, Sanchez LM. Seeing is Believing: Developing Multimodal Metabolic Insights at the Molecular Level. ACS CENTRAL SCIENCE 2024; 10:758-774. [PMID: 38680555 PMCID: PMC11046475 DOI: 10.1021/acscentsci.3c01438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 05/01/2024]
Abstract
This outlook explores how two different molecular imaging approaches might be combined to gain insight into dynamic, subcellular metabolic processes. Specifically, we discuss how matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and stimulated Raman scattering (SRS) microscopy, which have significantly pushed the boundaries of imaging metabolic and metabolomic analyses in their own right, could be combined to create comprehensive molecular images. We first briefly summarize the recent advances for each technique. We then explore how one might overcome the inherent limitations of each individual method, by envisioning orthogonal and interchangeable workflows. Additionally, we delve into the potential benefits of adopting a complementary approach that combines both MSI and SRS spectro-microscopy for informing on specific chemical structures through functional-group-specific targets. Ultimately, by integrating the strengths of both imaging modalities, researchers can achieve a more comprehensive understanding of biological and chemical systems, enabling precise metabolic investigations. This synergistic approach holds substantial promise to expand our toolkit for studying metabolites in complex environments.
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Affiliation(s)
- Rahuljeet
S Chadha
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125 United States
| | - Jason A. Guerrero
- Department
of Chemistry and Biochemistry, University
of California, Santa Cruz, Santa
Cruz, California 95064 United States
| | - Lu Wei
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125 United States
| | - Laura M. Sanchez
- Department
of Chemistry and Biochemistry, University
of California, Santa Cruz, Santa
Cruz, California 95064 United States
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Nagano E, Odake K, Shimma S. An Alternative Method for Quantitative Mass Spectrometry Imaging ( q-MSI) of Dopamine Utilizing Fragments of Animal Tissue. Mass Spectrom (Tokyo) 2023; 12:A0128. [PMID: 37538447 PMCID: PMC10394126 DOI: 10.5702/massspectrometry.a0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023] Open
Abstract
Mass spectrometry imaging (MSI) is a well-known method for the ionization of molecules on tissue sections and the visualization of their localization. Recently, different sample preparation methods and new instruments have been used for MSI, and different molecules are becoming visible. On the other hand, although several quantification methods (q-MSI) have been proposed, there is still room for the development of a simplified procedure. Here, we have attempted to develop a reproducible and reliable quantification method using a calibration curve prepared from tissue debris of a frozen section of a sample when we trim the frozen blocks. We discuss the reproducibility of this method across different sample lots and the effect of the biological matrix (ion suppression) on our results. The quantitative performance was evaluated in terms of accuracy and relative standard deviation, and the reliability of the quantitative values obtained by matrix-assisted laser desorption/ionization-MSI was further evaluated by enzyme-linked immunosorbent assay (ELISA). Our q-MSI method for the quantification of dopamine in mouse brain tissue was found to be highly linear, accurate, and precise. The quantitative values obtained by MSI were found to be highly comparable (>85% similarity) to the results obtained by ELISA from the same tissue extracts.
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Affiliation(s)
- Erika Nagano
- Research and Development Division, Miruion Corporation, Ibaraki, Osaka 567–0085, Japan
| | - Kazuki Odake
- Research and Development Division, Miruion Corporation, Ibaraki, Osaka 567–0085, Japan
| | - Shuichi Shimma
- Research and Development Division, Miruion Corporation, Ibaraki, Osaka 567–0085, Japan
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565–0871, Japan
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